Dataset Information

Diagnostic and Phylogenetic Utility of the rDNA Internal Transcribed Spacer Sequences of Steinernema.

ABSTRACT: The ITS regions of 10 species of Steinernema were PCR amplified and directly sequenced. Restriction mapping of these sequences revealed diagnostic variation such that the number of cuts and the length of the resulting fragments can be used to diagnose Steinernema species. Nevertheless, identical fragment sizes produced by non-homologous restriction sites also were identified. Pronounced variation in sequence length and nucleotide composition resulted in optimized alignments containing extensive regions of dubious homology. Significant shifts in nucleotide base composition exist among taxa and appear to mirror evolutionary history. These shifts do not have an observable influence on phylogenetic reconstruction and are probably due to descent as opposed to convergence. Alignment instability and the presence of alignment-ambiguous regions had the greatest effect on phylogeny reconstruction. Our results support the taxonomic utility of the ITS region to diagnose nematode species of the genus Steinernema, and all sampled taxa show evidence (in the form of numerous autapomorphic characters) of lineage independence. However, the ITS region appears to be phylogenetically informative only for closely related sister species. High variability among more distantly related taxa preclude its use for confidently resolving relationships among all members of the genus.

SUBMITTER: Nguyen KB

PROVIDER: S-EPMC2638135 | biostudies-other | 2001 Jun

REPOSITORIES: biostudies-other

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Diagnostic and Phylogenetic Utility of the rDNA Internal Transcribed Spacer Sequences of Steinernema.

Nguyen K B KB Maruniak J J Adams B J BJ

Journal of nematology 20010601 2-3

The ITS regions of 10 species of Steinernema were PCR amplified and directly sequenced. Restriction mapping of these sequences revealed diagnostic variation such that the number of cuts and the length of the resulting fragments can be used to diagnose Steinernema species. Nevertheless, identical fragment sizes produced by non-homologous restriction sites also were identified. Pronounced variation in sequence length and nucleotide composition resulted in optimized alignments containing extensive ...[more]

PMID: 19266001

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Project description:BACKGROUND: Most phylogenetic studies using current methods have focused on primary DNA sequence information. However, RNA secondary structures are particularly useful in systematics because they include characteristics, not found in the primary sequence, that give "morphological" information. Despite the number of recent molecular studies on octocorals, there is no consensus opinion about a region that carries enough phylogenetic resolution to solve intrageneric or close species relationships. Moreover, intrageneric morphological information by itself does not always produce accurate phylogenies; intra-species comparisons can reveal greater differences than intra-generic ones. The search for new phylogenetic approaches, such as by RNA secondary structure analysis, is therefore a priority in octocoral research. RESULTS: Initially, twelve predicted RNA secondary structures were reconstructed to provide the basic information for phylogenetic analyses; they accorded with the 6 helicoidal ring model, also present in other groups of corals and eukaryotes. We obtained three similar topologies for nine species of the Caribbean gorgonian genus Eunicea (candelabrum corals) with two sister taxa as outgroups (genera Plexaura and Pseudoplexaura) on the basis of molecular morphometrics of ITS2 RNA secondary structures only, traditional primary sequence analyses and maximum likelihood, and a Bayesian analysis of the combined data. The latter approach allowed us to include both primary sequence and RNA molecular morphometrics; each data partition was allowed to have a different evolution rate. In addition, each helix was partitioned as if it had evolved at a distinct rate. Plexaura flexuosa was found to group within Eunicea; this was best supported by both the molecular morphometrics and combined analyses. We suggest Eunicea flexuosa (Lamouroux, 1821) comb. nov., and we present a new species description including Scanning Electron Microscopy (SEM) images of morphological characteristics (sclerites). Eunicea flexuosa, E. pallida, E. laxispica and E. mammosa formed a separate clade in the molecular phylogenies, and were reciprocally monophyletic with respect to other Eunicea (Euniceopsis subgenus, e.g. E. tourneforti and E. laciniata) in the molecular morphometrics tree, with the exception of E. fusca. Moreover, we suggest a new diagnostic character for Eunicea, also present in E. flexuosa: middle layer sclerites > 1 mm in length. CONCLUSION: ITS2 was a reliable sequence for intrageneric studies in gorgonian octocorals because of the amount of phylogenetic signal, and was corroborated against morphological characters separating Eunicea from Plexaura. The ITS2 RNA secondary structure approach to phylogeny presented here did not rely on alignment methods such as INDELS, but provided clearly homologous characters for partition analysis and RNA molecular morphometrics. These approaches support the divergence of Eunicea flexuosa comb. nov. from the outgroup Plexaura, although it has been considered part of this outgroup for nearly two centuries because of morphological resemblance.

Dataset Information

Diagnostic and Phylogenetic Utility of the rDNA Internal Transcribed Spacer Sequences of Steinernema.

Publications

Diagnostic and Phylogenetic Utility of the rDNA Internal Transcribed Spacer Sequences of Steinernema.

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